My hope is that this is simple miscommunication. It does not take a rocket scientist to know that clear caulk on the interior prior to staining will yield a nice stripe of unstained surface which is undesirable. The interior really should not be caulked at all until after staining IMO.

Yes, his statement would certainly raise more questions than it answers if there is no miscommunication.

Install the windows, seal , insulate, and caulk the outside. Do not caulk the interior until it is stained. HomeSealed is 100% correct.

patient really need any call game with the wood window.

I meant to say caulking really isn't needed with a wood window especially if the wood is stained.

Caulking on the interior is traditionally for aesthetics, and on wood windows that is not kosher. No caulk for you!